The anaerobic oxidation of methane and higher C2+ alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. Although these processes fuel a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral assemblages in long-term sediment-free enrichments of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes (AMGs) directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of candidate AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also examined potential host-virus pairs using CRISPR- and tRNA-based methods. Lastly, we identified the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of new viruses obtained from these multi-year enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.
", "doi": "10.1093/ismejo/wrag172", "pmcid": "PMC13452462", "issn": "1751-7362", "publisher": "Oxford University Press (OUP)", "publication": "The ISME Journal", "publication_date": "2026-07-01", "series_number": "1", "volume": "20", "issue": "1", "pages": "wrag172" }, { "id": "authors:eph09-mrq50", "collection": "authors", "collection_id": "eph09-mrq50", "cite_using_url": "https://authors.library.caltech.edu/records/eph09-mrq50", "type": "article", "title": "Deep-sea anaerobic microbial communities couple degradation of insoluble chitin to extracellular electron transfer", "author": [ { "family_name": "Jangir", "given_name": "Yamini", "orcid": "0000-0002-2779-9049", "clpid": "Jangir-Yamini" }, { "family_name": "Guo", "given_name": "Yongzhao", "orcid": "0009-0005-3983-8382", "clpid": "Guo-Yongzhao" }, { "family_name": "Connon", "given_name": "Stephanie", "clpid": "Connon-Stephanie-A" }, { "family_name": "Pontrelli", "given_name": "Sammy", "orcid": "0000-0001-6265-8842" }, { "family_name": "Wu", "given_name": "Fabai", "orcid": "0000-0001-5812-5621", "clpid": "Wu-Fabai" }, { "family_name": "Schwartzman", "given_name": "Julia", "orcid": "0000-0003-4563-4835" }, { "family_name": "Lim", "given_name": "Sujung", "orcid": "0000-0001-6040-729X", "clpid": "Lim-Sujung" }, { "family_name": "Sauer", "given_name": "Uwe", "orcid": "0000-0002-5923-0770" }, { "family_name": "Cordero", "given_name": "Otto X", "orcid": "0000-0002-2695-270X" }, { "family_name": "Orphan", "given_name": "Victoria J", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Chitin, a major structural component of arthropod exoskeletons, is an abundant carbon and nitrogen source in marine ecosystems. While its degradation is well studied in oxic waters, the microbial processes and interactions that mediate its anaerobic breakdown in deep-sea sediments remain poorly understood. Iron oxides are predicted to be energetically favorable electron acceptors for anaerobic chitin degradation, yet the spatial separation of insoluble substrates and the required microbial partnerships in sediments are not well defined. Here, we used potentiostatically controlled bioelectrochemical reactors poised at +0.22 V vs. Standard Hydrogen Electrode, mimicking iron-reducing conditions, to enrich and characterize a chitin-degrading, metal-reducing microbial community from an anoxic deep-sea whale-fall sediment. Amendment with crystalline chitin generated stable anodic currents, which increased upon addition of chitin-associated metabolites (N-acetylglucosamine, glucose, acetate). 16S rRNA gene sequencing revealed a deep-sea affiliated assemblage dominated by Firmicutes (Vallitalea), Spirochaetota, Gammaproteobacteria, and Desulfobacterota (Trichloromonas). Exoenzyme assays, metabolite profiling, and current measurements confirmed that active chitin degradation provided substrate(s) for extracellular electron transfer (EET). Single-cell analyses using FISH-BONCAT and nanoSIMS showed that Vallitalea (primary degrader) and electrode-respiring Desulfobacterota exhibited highest activity within the electrode biofilm, particularly within ca.10 μm of the surface. We isolated a chitin-degrading Vallitalea sp. and an iron-reducing, electrogenic Trichloromonas sp., and demonstrated that, when reconstituted in co-culture, they cooperatively degrade chitin via acetate cross-feeding coupled to EET. This integrated electrochemical and ecophysiological study reveals microbial interactions linking chitin degradation with iron-oxide respiration in deep-sea sediments and provides a defined electrogenic model community for future syntrophy research.
", "doi": "10.1093/ismejo/wrag151", "pmcid": "PMC13374861", "issn": "1751-7362", "publisher": "Oxford University Press (OUP)", "publication": "The ISME Journal", "publication_date": "2026-06-15", "series_number": "1", "volume": "20", "issue": "1", "pages": "wrag151" }, { "id": "authors:vqfbv-b9035", "collection": "authors", "collection_id": "vqfbv-b9035", "cite_using_url": "https://authors.library.caltech.edu/records/vqfbv-b9035", "type": "article", "title": "Distinct microbial communities within and on seep carbonates support long-term anaerobic oxidation of methane and divergent pMMO diversity", "author": [ { "family_name": "Mayr", "given_name": "Magdalena J.", "orcid": "0000-0002-3182-1480", "clpid": "Mayr-Magdalena-J" }, { "family_name": "Parra", "given_name": "Sergio A.", "orcid": "0000-0002-2637-7960", "clpid": "Parra-Sergio-A" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Narayanan", "given_name": "Aditi K.", "orcid": "0000-0003-0627-1859", "clpid": "Narayanan-Aditi-K" }, { "family_name": "Murali", "given_name": "Ranjani", "orcid": "0000-0003-4073-9910", "clpid": "Murali-Ranjani" }, { "family_name": "Cr\u00e9mi\u00e8re", "given_name": "Antoine", "orcid": "0000-0001-7382-2097", "clpid": "Cr\u00e9mi\u00e8re-Antoine" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "At methane seeps worldwide, syntrophic anaerobic methane-oxidizing archaea and sulfate-reducing bacteria promote carbonate precipitation and rock formation, acting as methane and carbon sinks. Although maintenance of anaerobic oxidation of methane (AOM) within seep carbonates has been documented, its reactivation upon methane exposure remains uncertain. Surface-associated microbes may metabolize sulfide from AOM, maintain carbonate anoxia, contribute to carbonate dissolution, and support higher trophic levels; however, these communities are poorly described. We provide insights into microbial diversity, metabolism, activity, and resiliency within and on seep carbonates through amplicon and metagenomic sequencing, incubations, and non-canonical amino acid tagging combined with fluorescence in situ hybridization (BONCAT-FISH). Ca. Methanophaga (ANME-1) dominated the carbonate interiors in active and low activity seeps, co-occurring with Ca. Desulfaltia as main sulfate reducer, potentially a new syntrophic partner in AOM. Single-cell BONCAT-FISH revealed variability in ANME-1 activity, suggesting potential dormancy in carbonates from low activity seep sites. However, incubations with carbonates from low activity seeps (≥24 months) showed exponential AOM reactivation (~44-day doubling), suggesting these carbonates retain the potential as long-term methane sinks under dynamic seepage conditions. Surface-associated microbial communities were heterogeneous and distinct from the carbonate interior and other seep habitats. Anaerobic methane-oxidizing biofilms and sulfide-oxidizing mats were associated with carbonates with high and intermediate AOM rates potentially influencing carbonate precipitation/dissolution. Shared aerobic methanotrophs between carbonate surfaces and invertebrates indicated carbonate surfaces may represent animal epibiont reservoirs. Recovered particulate methane monooxygenases included both aerobic methanotrophs and divergent forms associated with the Methylophagaceae, suggesting a new function in this group.
", "doi": "10.1093/ismejo/wraf153", "pmcid": "PMC12422003", "issn": "1751-7362", "publisher": "Oxford University Press (OUP)", "publication": "The ISME Journal", "publication_date": "2025-09-05", "series_number": "1", "volume": "19", "issue": "1", "pages": "wraf153" }, { "id": "authors:9x30e-z5459", "collection": "authors", "collection_id": "9x30e-z5459", "cite_using_url": "https://authors.library.caltech.edu/records/9x30e-z5459", "type": "article", "title": "CABO-16S\u2014a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples", "author": [ { "family_name": "Eitel", "given_name": "Eryn\u00a0M.", "orcid": "0009-0007-2391-9297", "clpid": "Eitel-Eryn-M" }, { "family_name": "Utter", "given_name": "Daniel\u00a0R.", "orcid": "0000-0003-3322-7108", "clpid": "Utter-Daniel-R" }, { "family_name": "Connon", "given_name": "Stephanie\u00a0A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Murali", "given_name": "Ranjani", "orcid": "0000-0003-4073-9910", "clpid": "Murali-Ranjani" } ], "abstract": "Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by the need for additional sequencing to obtain separate 16S and 18S ribosomal RNA (rRNA) amplicons or the constraints imposed by \"universal\" primers. Organellar 16S rRNA sequences are amplified and sequenced along with prokaryote 16S rRNA and provide an alternative method to identify eukaryotic microorganisms. CABO-16S combines bacterial and archaeal sequences from the SILVA database with 16S rRNA sequences of plastids and other organelles from the PR2 database to enable identification of all 16S rRNA sequences. Comparison of CABO-16S with SILVA 138.2 results in equivalent taxonomic classification of mock communities and increased classification of diverse environmental samples. In particular, identification of phototrophic eukaryotes in shallow seagrass environments, marine waters, and lake waters was increased. The CABO-16S framework allows users to add custom sequences for further classification of underrepresented clades and can be easily updated with future releases of reference databases. Addition of sequences obtained from Sanger sequencing of methane seep sediments and curated sequences of the polyphyletic SEEP-SRB1 clade resulted in differentiation of syntrophic and non-syntrophic SEEP-SRB1 in hydrothermal vent sediments. CABO-16S highlights the benefit of combining and amending existing training sets when studying microorganisms in diverse environments.
", "doi": "10.1093/nargab/lqaf061", "pmcid": "PMC12086536", "issn": "2631-9268", "publisher": "Oxford University Press (OUP)", "publication": "NAR Genomics and Bioinformatics", "publication_date": "2025-06", "series_number": "2", "volume": "7", "issue": "2", "pages": "lqaf061" }, { "id": "authors:tse8x-ay919", "collection": "authors", "collection_id": "tse8x-ay919", "cite_using_url": "https://authors.library.caltech.edu/records/tse8x-ay919", "type": "article", "title": "Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea", "author": [ { "family_name": "Murali", "given_name": "Ranjani", "orcid": "0000-0003-4073-9910", "clpid": "Murali-Ranjani" }, { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Wu", "given_name": "Fabai", "orcid": "0000-0001-5812-5621", "clpid": "Wu-Fabai" }, { "family_name": "Metcalfe", "given_name": "Kyle S.", "orcid": "0000-0002-2963-765X", "clpid": "Metcalfe-Kyle-S" }, { "family_name": "Cr\u00e9mi\u00e8re", "given_name": "Antoine", "orcid": "0000-0001-7382-2097", "clpid": "Cr\u00e9mi\u00e8re-Antoine" }, { "family_name": "Laso-P\u00e8rez", "given_name": "Rafael", "orcid": "0000-0002-6912-7865", "clpid": "Laso-P\u00e8rez-Rafael" }, { "family_name": "Malmstrom", "given_name": "Rex R.", "orcid": "0000-0002-4758-7369", "clpid": "Malmstrom-Rex-R" }, { "family_name": "Goudeau", "given_name": "Danielle", "orcid": "0000-0002-3785-032X", "clpid": "Goudeau-Danielle" }, { "family_name": "Woyke", "given_name": "Tanja", "orcid": "0000-0002-9485-5637", "clpid": "Woyke-Tanja" }, { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-Roland" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.", "doi": "10.1371/journal.pbio.3002292", "pmcid": "PMC10553843", "issn": "1545-7885", "publisher": "Public Library of Science", "publication": "PLOS Biology", "publication_date": "2023-09", "series_number": "9", "volume": "21", "issue": "9", "pages": "e3002292" }, { "id": "authors:cee4z-fzt63", "collection": "authors", "collection_id": "cee4z-fzt63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220405-464784300", "type": "article", "title": "Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily", "author": [ { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Yu", "given_name": "Feiqiao B.", "orcid": "0000-0003-3416-3046", "clpid": "Yu-Feiqiao-B" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Lim", "given_name": "Sujung", "orcid": "0000-0001-6040-729X", "clpid": "Lim-Sujung" }, { "family_name": "Magyar", "given_name": "John S.", "orcid": "0000-0002-3586-8286", "clpid": "Magyar-John-S" }, { "family_name": "Pe\u00f1a-Salinas", "given_name": "Manet E.", "orcid": "0000-0002-5835-0455", "clpid": "Pe\u00f1a-Salinas-Manet-E" }, { "family_name": "Quake", "given_name": "Stephen R.", "orcid": "0000-0002-1613-0809", "clpid": "Quake-Stephen-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400\u2009km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.", "doi": "10.1038/s41396-022-01222-x", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2022-07", "volume": "16", "pages": "1750-1764" }, { "id": "authors:bza61-q9r11", "collection": "authors", "collection_id": "bza61-q9r11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220721-8119000", "type": "article", "title": "Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep", "author": [ { "family_name": "Yu", "given_name": "Hang", "orcid": "0000-0002-7600-1582", "clpid": "Yu-Hang-ENV" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Goudeau", "given_name": "Danielle", "orcid": "0000-0002-3785-032X", "clpid": "Goudeau-Danielle" }, { "family_name": "Malmstrom", "given_name": "Rex R.", "orcid": "0000-0002-4758-7369", "clpid": "Malmstrom-Rex-R" }, { "family_name": "Woyke", "given_name": "Tanja", "orcid": "0000-0002-9485-5637", "clpid": "Woyke-Tanja" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b (\"Candidatus Methanocomedenaceae\") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses.", "doi": "10.1128/aem.02109-21", "pmcid": "PMC9195934", "issn": "0099-2240", "publisher": "American Society for Microbiology", "publication": "Applied and Environmental Microbiology", "publication_date": "2022-06-14", "series_number": "11", "volume": "88", "issue": "11", "pages": "Art. No. e0210921" }, { "id": "authors:z8b1y-75771", "collection": "authors", "collection_id": "z8b1y-75771", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220118-973186300", "type": "article", "title": "Unique mobile elements and scalable gene flow at the prokaryote\u2013eukaryote boundary revealed by circularized Asgard archaea genomes", "author": [ { "family_name": "Wu", "given_name": "Fabai", "orcid": "0000-0001-5812-5621", "clpid": "Wu-Fabai" }, { "family_name": "Speth", "given_name": "Daan R.", "orcid": "0000-0002-2361-5935", "clpid": "Speth-Daan-R" }, { "family_name": "Philosof", "given_name": "Alon", "orcid": "0000-0003-2684-8678", "clpid": "Philosof-Alon" }, { "family_name": "Cr\u00e9mi\u00e8re", "given_name": "Antoine", "orcid": "0000-0001-7382-2097", "clpid": "Cr\u00e9mi\u00e8re-Antoine" }, { "family_name": "Narayanan", "given_name": "Aditi", "clpid": "Narayanan-Aditi" }, { "family_name": "Barco", "given_name": "Roman A.", "clpid": "Barco-Roman-A" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Amend", "given_name": "Jan P.", "orcid": "0000-0003-4953-7776", "clpid": "Amend-Jan-P" }, { "family_name": "Antoshechkin", "given_name": "Igor A.", "orcid": "0000-0002-9934-3040", "clpid": "Antoshechkin-Igor-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation\u2013decentralized innovation\u2013hierarchical import model that accounts for the emergence of eukaryotic complexity.", "doi": "10.1038/s41564-021-01039-y", "issn": "2058-5276", "publisher": "Nature Publishing Group", "publication": "Nature Microbiology", "publication_date": "2022-02", "series_number": "2", "volume": "7", "issue": "2", "pages": "200-212" }, { "id": "authors:vbj9s-6jr73", "collection": "authors", "collection_id": "vbj9s-6jr73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200413-101943907", "type": "article", "title": "Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy", "author": [ { "family_name": "Metcalfe", "given_name": "Kyle S.", "orcid": "0000-0002-2963-765X", "clpid": "Metcalfe-Kyle-S" }, { "family_name": "Murali", "given_name": "Ranjani", "orcid": "0000-0003-4073-9910", "clpid": "Murali-Ranjani-S" }, { "family_name": "Mullin", "given_name": "Sean W.", "orcid": "0000-0002-6225-3279", "clpid": "Mullin-Sean-W" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "Archaeal anaerobic methanotrophs (\"ANME\") and sulfate-reducing Deltaproteobacteria (\"SRB\") form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b\u2014SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b\u2014SEEP-SRB1g consortia incubated with a headspace containing CH\u2084 and \u00b9\u2075N\u2082 revealed differences in cellular \u00b9\u2075N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in \u00b9\u2075N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.", "doi": "10.1038/s41396-020-00757-1", "pmcid": "PMC8027057", "issn": "1751-7362", "publisher": "Nature Publishing Group", "publication": "ISME Journal", "publication_date": "2021-02", "series_number": "2", "volume": "15", "issue": "2", "pages": "377-396" }, { "id": "authors:9gq6z-05s57", "collection": "authors", "collection_id": "9gq6z-05s57", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160628-092522305", "type": "article", "title": "Visualizing in situ translational activity for identifying and sorting slow-growing archaeal\u2212bacterial consortia", "author": [ { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-Roland" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Goudeau", "given_name": "Danielle", "orcid": "0000-0002-3785-032X", "clpid": "Goudeau-Danielle" }, { "family_name": "Malmstrom", "given_name": "Rex R.", "orcid": "0000-0002-4758-7369", "clpid": "Malmstrom-Rex-R" }, { "family_name": "Woykeb", "given_name": "Tanja", "clpid": "Woykeb-Tanja" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.", "doi": "10.1073/pnas.1603757113", "pmcid": "PMC4948357", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2016-07-12", "series_number": "28", "volume": "113", "issue": "28", "pages": "E4069-E4078" }, { "id": "authors:fr4a3-3bm16", "collection": "authors", "collection_id": "fr4a3-3bm16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141111-104738855", "type": "article", "title": "Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs", "author": [ { "family_name": "Tavormina", "given_name": "Patricia L.", "clpid": "Tavormina-Patricia-L" }, { "family_name": "Hatzenpichler", "given_name": "Roland", "orcid": "0000-0002-5489-3444", "clpid": "Hatzenpichler-Roland" }, { "family_name": "McGlynn", "given_name": "Shawn E.", "orcid": "0000-0002-8199-7011", "clpid": "McGlynn-Shawn-E" }, { "family_name": "Chadwick", "given_name": "Grayson L.", "orcid": "0000-0003-0700-9350", "clpid": "Chadwick-Grayson-L" }, { "family_name": "Dawson", "given_name": "Katherine S.", "orcid": "0000-0001-8856-4609", "clpid": "Dawson-Katherine-S" }, { "family_name": "Connon", "given_name": "Stephanie A.", "clpid": "Connon-Stephanie-A" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "abstract": "We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1, \"whale fall 1\" that shares 98% 16S rRNA identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep sea mussels, 94.6% 16S rRNA identity with Methylobacter species, and 93.6% 16S rRNA identity with Methylomonas and Methylosarcina species. Strain WF1 represents the first cultivar from the 'Deep Sea 1' clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. WF1 cells were elongated cocci approximately 1.5 \u00b5m in diameter, and occurred singly, in pairs and clumps. The cell wall was Gram negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic GC content of WF1 was 40.5%, significantly lower than currently described cultivars, and the major fatty acids were 16:0, 16:1 \u03c99c, 16:1 \u03c99t, 16:1 \u03c98c and 16:2 \u03c99, 14. Growth occurred in liquid media at an optimal temperature of 23oC, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1, a capacity that had not been functionally demonstrated in members of Methylobacter. On the basis of unique morphological, physiological, and phylogenetic properties this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti (type strain WF1 = BCCM LMG 28393 = ATCC BAA-2619).", "doi": "10.1099/ijs.0.062927-0", "issn": "1466-5026", "publisher": "International Union of Microbiological Societies", "publication": "International Journal of Systematic and Evolutionary Microbiology", "publication_date": "2015-01", "series_number": "1", "volume": "65", "issue": "1", "pages": "251-259" } ]